Knowledge-based energy functions for computational studies of proteins

This chapter discusses theoretical framework and methods for developing knowledge-based potential functions essential for protein structure prediction, protein-protein interaction, and protein sequence design. We discuss in some details about the Miyazawa-Jernigan contact statistical potential, distance-dependent statistical potentials, as well as geometric statistical potentials. We also describe a geometric model for developing both linear and non-linear potential functions by optimization. Applications of knowledge-based potential functions in protein-decoy discrimination, in protein-protein interactions, and in protein design are then described. Several issues of knowledge-based potential functions are finally discussed.Comment: 57 pages, 6 figures. To be published in a book by Springe

Local Helioseismology of Sunspots: Current Status and Perspectives (Invited Review)

Mechanisms of the formation and stability of sunspots are among the longest-standing and intriguing puzzles of solar physics and astrophysics. Sunspots are controlled by subsurface dynamics hidden from direct observations. Recently, substantial progress in our understanding of the physics of the turbulent magnetized plasma in strong-field regions has been made by using numerical simulations and local helioseismology. Both the simulations and helioseismic measurements are extremely challenging, but it becomes clear that the key to understanding the enigma of sunspots is a synergy between models and observations. Recent observations and radiative MHD numerical models have provided a convincing explanation to the Evershed flows in sunspot penumbrae. Also, they lead to the understanding of sunspots as self-organized magnetic structures in the turbulent plasma of the upper convection zone, which are maintained by a large-scale dynamics. Local helioseismic diagnostics of sunspots still have many uncertainties, some of which are discussed in this review. However, there have been significant achievements in resolving these uncertainties, verifying the basic results by new high-resolution observations, testing the helioseismic techniques by numerical simulations, and comparing results obtained by different methods. For instance, a recent analysis of helioseismology data from the Hinode space mission has successfully resolved several uncertainties and concerns (such as the inclined-field and phase-speed filtering effects) that might affect the inferences of the subsurface wave-speed structure of sunspots and the flow pattern. It becomes clear that for the understanding of the phenomenon of sunspots it is important to further improve the helioseismology methods and investigate the whole life cycle of active regions, from magnetic-flux emergence to dissipation.Comment: 34 pages, 18 figures, submitted to Solar Physic

Measurements of differential production cross sections for a Z boson in association with jets in pp collisions at root s=8 TeV

Peer reviewe

Search for the associated production of the Higgs boson with a top-quark pair

A search for the standard model Higgs boson produced in association with a top-quark pair t t ¯ H (tt¯H) is presented, using data samples corresponding to integrated luminosities of up to 5.1 fb −1 and 19.7 fb −1 collected in pp collisions at center-of-mass energies of 7 TeV and 8 TeV respectively. The search is based on the following signatures of the Higgs boson decay: H → hadrons, H → photons, and H → leptons. The results are characterized by an observed t t ¯ H tt¯H signal strength relative to the standard model cross section, μ = σ/σ SM ,under the assumption that the Higgs boson decays as expected in the standard model. The best fit value is μ = 2.8 ± 1.0 for a Higgs boson mass of 125.6 GeV

Search for neutral resonances decaying into a Z boson and a pair of b jets or τ leptons

A search is performed for a new resonance decaying into a lighter resonance and a Z boson. Two channels are studied, targeting the decay of the lighter resonance into either a pair of oppositely charged τ leptons or a bb‾ pair. The Z boson is identified via its decays to electrons or muons. The search exploits data collected by the CMS experiment at a centre-of-mass energy of 8 TeV, corresponding to an integrated luminosity of 19.8 fb −1 . No significant deviations are observed from the standard model expectation and limits are set on production cross sections and parameters of two-Higgs-doublet models

Search for vectorlike charge 2/3 T quarks in proton-proton collisions at root(s)=8 TeV

Peer reviewe

Measurement of the t-channel single-top-quark production cross section and of the |Vtb| CKM matrix element in pp collisions at SQR = 8 TeV

Measurements are presented of the t -channel single-top-quark production cross section in proton-proton collisions at s√ = 8 TeV. The results are based on a data sample corresponding to an integrated luminosity of 19.7 fb −1 recorded with the CMS detector at the LHC. The cross section is measured inclusively, as well as separately for top (t) and antitop (t¯) , in final states with a muon or an electron. The measured inclusive t -channel cross section is σ t -ch. = 83 . 6 ± 2 . 3 (stat.) ± 7 . 4 (syst.) pb. The single t and t¯ cross sections are measured to be σ t -ch. ( t ) = 53 . 8 ± 1 . 5 (stat.) ± 4 . 4 (syst.) pb and σ t -ch. (t¯) = 27 . 6 ± 1 . 3 (stat.) ± 3 . 7 (syst.) pb, respectively. The measured ratio of cross sections is R t -ch. = σ t -ch. (t) /σ t -ch. (t¯) = 1 . 95 ± 0 . 10 (stat.) ± 0 . 19 (syst.), in agreement with the standard model prediction. The modulus of the Cabibbo-Kobayashi-Maskawa matrix element V tb is extracted and, in combination with a previous CMS result at s√ = 7 TeV, a value | V tb | = 0 . 998 ± 0 . 038 (exp.) ± 0 . 016 (theo.) is obtained

Search for a low-mass pseudoscalar Higgs boson produced in association with a bb⁻ pair in pp collisions at √s=8 TeV

A search is reported for a light pseudoscalar Higgs boson decaying to a pair of tau leptons, produced in association with a b (b) over bar pair, in the context of two-Higgs-doublet models. The results are based on pp collision data at a centre-of-mass energy of 8 TeV collected by the CMS experiment at the LHC and corresponding to an integrated luminosity of 19.7 fb(-1). Pseudoscalar boson masses between 25 and 80 GeV are probed. No evidence for a pseudoscalar boson is found and upper limits are set on the product of cross section and branching fraction to tau pairs between 7 and 39 pb at the 95% confidence level. This excludes pseudoscalar A bosons with masses between 25 and 80 GeV, with SM-like Higgs boson negative couplings to down-type fermions, produced in association with bb pairs, in Type II, two-Higgs-doublet models. (C) 2016 The Author(s). Published by Elsevier B.V. This is an open access article under the CC BY license (http://creativecommonnorg/licensesiby/4.01)